CM5 Sensor Chip Research Articles

Glycogen Synthase Kinase 3β Interaction Protein Functions as an A-kinase Anchoring Protein

A-kinase anchoring proteins (AKAPs) include a family of scaffolding proteins that target protein kinase A (PKA) and other signaling proteins to cellular compartments and thereby confine the activities of the associated proteins to distinct regions within cells. AKAPs bind PKA directly. The interaction is mediated by the dimerization and docking domain of regulatory subunits of PKA and the PKA-binding domain of AKAPs. Analysis of the interactions between the dimerization and docking domain and various PKA-binding domains yielded a generalized motif allowing the identification of AKAPs. Our bioinformatics and peptide array screening approaches based on this signature motif identified GSKIP (glycogen synthase kinase 3beta interaction protein) as an AKAP. GSKIP directly interacts with PKA and GSK3beta (glycogen synthase kinase 3beta). It is widely expressed and facilitates phosphorylation and thus inactivation of GSK3beta by PKA. GSKIP contains the evolutionarily conserved domain of unknown function 727. We show here that this domain of GSKIP and its vertebrate orthologues binds both PKA and GSK3beta and thereby provides a mechanism for the integration of PKA and GSK3beta signaling pathways.

PB1 Domain Interaction of p62/Sequestosome 1 and MEKK3 Regulates NF-κB Activation

p62/Sequestosome 1 is a scaffold protein involved in the regulation of autophagy, trafficking of proteins to the proteasome, and activation of NF-kappaB. p62 encodes an N-terminal PB1 domain in addition to the ZZ domain, TRAF6-binding domain, LC3 interaction region, and ubiquitin-associated domain, each critical for the physiological function of p62. PB1 domains have a beta-grasp topology where the front end of one PB1 domain binds the back end of a second PB1 domain. The p62 PB1 domain homodimerizes as well as heterodimerizes with other PB1 domains. The front end of the PB1 domain in p62 binds the PB1 domain of atypical protein kinases C, the MAPK kinase, MEK5, and the NBR1 protein. Other than its role in homodimerization, the rear end acidic cluster region of the p62 PB1 domain had no previous defined binding partners. Herein, we demonstrate that the rear end acidic cluster region of the p62 PB1 domain binds the front end basic region of the MAPK kinase kinase, MEKK3. p62 and MEKK3 co-localize in speckles or aggregates that are centers for organizing TRAF6-regulated NF-kappaB signaling and the assembly of polyubiquinated proteins sorting to sequestosomes and proteasomes. The p62-MEKK3 complex binds TRAF6, which regulates the ubiquitination of the IKK complex and NF-kappaB activation. p62 is required for the association of MEKK3 with TRAF6 and short hairpin RNA knockdown of p62 inhibits IL-1 and MEKK3 activation of NF-kappaB. The rear end acidic cluster of the p62 PB1 domain is used to organize cytosolic aggregates or speckles-associated TRAF6-p62-MEKK3 complex for control of NF-kappaB activation.

Analyze the bioactivity of PD-1 and PD-L1 recombination protein which expressed by prokaryotic system

To analyze the interaction of PD-1 and PD-L1 recombination protein and to know their bioactivity and affinity. Stick the PD-1 protein on the surface of CM5 sensor chip by the method of Ammine coupling after being preconsentrated. Dilute the PD-L1 protein step by step and reject it to the passage on CM5 sensor chip which had been stick by PD-1. The time of combination is 3 minutes and of separation is 15 minutes, respectively. Observe the procession and analyze data by BIA Evaluation software 4. On the consistency of 40 microg/ml, pH 4.5, the PD-1 protein could couple steady on the surface of CM5sensor chip, RU is 3300. On the density of 200 mmol/ml PD-L1 could combine with PD-1 specifically, RU = 150, K(D) = 3.5 x 10(-6). The PD-1 and PD-L1 recombination protein which we expressed by prokaryotic system have good affinity and bioactivity. The results could provide basic condition for later study.

Germ Line-governed Recognition of a Cancer Epitope by an Immunodominant Human T-cell Receptor

CD8(+) T-cells specific for MART-1-(26-35), a dominant melanoma epitope restricted by human leukocyte antigen (HLA)-A*0201, are exceptionally common in the naive T-cell repertoire. Remarkably, the TRAV12-2 gene is used to encode the T-cell receptor alpha (TCRalpha) chain in >87% of these T-cells. Here, the molecular basis for this genetic bias is revealed from the structural and thermodynamic properties of an archetypal TRAV12-2-encoded TCR complexed to the clinically relevant heteroclitic peptide, ELAGIGILTV, bound to HLA-A*0201 (A2-ELA). Unusually, the TRAV12-2 germ line-encoded regions of the TCR dominate the major atomic contacts with the peptide at the TCR/A2-ELA interface. This "innate" pattern of antigen recognition probably explains the unique characteristics and extraordinary frequencies of CD8(+) T-cell responses to this epitope.

Synergy between Ficolin-2 and Pentraxin 3 Boosts Innate Immune Recognition and Complement Deposition

The long pentraxin 3 (PTX3) is a multifunctional soluble pattern recognition molecule that is crucial in innate immune protection against opportunistic fungal pathogens such as Aspergillus fumigatus. The mechanisms that mediate downstream effects of PTX3 are largely unknown. However, PTX3 interacts with C1q from the classical pathway of the complement. The ficolins are recognition molecules of the lectin complement pathway sharing structural and functional characteristics with C1q. Thus, we investigated whether the ficolins (Ficolin-1, -2, and -3) interact with PTX3 and whether the complexes are able to modulate complement activation on A. fumigatus. Ficolin-2 could be affinity-isolated from human plasma on immobilized PTX3. In binding studies, Ficolin-1 and particularly Ficolin-2 interacted with PTX3 in a calcium-independent manner. Ficolin-2, but not Ficolin-1 and Ficolin-3, bound A. fumigatus directly, but this binding was enhanced by PTX3 and vice versa. Ficolin-2-dependent complement deposition on the surface of A. fumigatus was enhanced by PTX3. A polymorphism in the FCN2 gene causing a T236M amino acid change in the fibrinogen-like binding domain of Ficolin-2, which affects the binding to GlcNAc, reduced Ficolin-2 binding to PTX3 and A. fumigatus significantly. These results demonstrate that PTX3 and Ficolin-2 may recruit each other on pathogens. The effect was alleviated by a common amino acid change in the fibrinogen-like domain of Ficolin-2. Thus, components of the humoral innate immune system, which activate different complement pathways, cooperate and amplify microbial recognition and effector functions.

Molecular Interplay between Endostatin, Integrins, and Heparan Sulfate

Endostatin is an endogenous inhibitor of angiogenesis. Although several endothelial cell surface molecules have been reported to interact with endostatin, its molecular mechanism of action is not fully elucidated. We used surface plasmon resonance assays to characterize interactions between endostatin, integrins, and heparin/heparan sulfate. alpha5beta1 and alphavbeta3 integrins form stable complexes with immobilized endostatin (KD=approximately 1.8x10(-8) M, two-state model). Two arginine residues (Arg27 and Arg139) are crucial for the binding of endostatin to integrins and to heparin/heparan sulfate, suggesting that endostatin would not bind simultaneously to integrins and to heparan sulfate. Experimental data and molecular modeling support endostatin binding to the headpiece of the alphavbeta3 integrin at the interface between the beta-propeller domain of the alphav subunit and the betaA domain of the beta3 subunit. In addition, we report that alpha5beta1 and alphavbeta3 integrins bind to heparin/heparan sulfate. The ectodomain of the alpha5beta1 integrin binds to haparin with high affinity (KD=15.5 nM). The direct binding between integrins and heparin/heparan sulfate might explain why both heparan sulfate and alpha5beta1 integrin are required for the localization of endostatin in endothelial cell lipid rafts.

Detection of microcystins in environmental samples using surface plasmon resonance biosensor

An indirect inhibitive surface plasmon resonance (SPR) immunoassay was developed for the microcystins (MCs) detection. The bioconjugate of MC-LR and bovine serum albumin (BSA) was immobilized on a CM5 sensor chip. A serial premixture of MC-LR standards (or samples) and monoclonal antibody (mAb) were injected over the functional sensor surface, and the subsequent specific immunoreaction was monitored on the BIAcore 3000 biosensor and generated a signal with an increasing intensity in response to the decreasing MCs concentration. The developed SPR immunoassay has a wide quantitative range in 1–100 μg L −1. Although not as sensitive as conventional enzyme-linked immunosorbent assay (ELISA), the SPR biosensor offered unique advantages: (1) the sensor chip could be reusable without any significant loss in its binding activity after 50 assay-regeneration cycles, (2) one single assay could be accomplished in 50 min (including 30-min preincubation and 20-min BIAcore analysis), and (3) this method did not require multiple steps. The SPR biosensor was also used to detect MCs in environmental samples, and the results compared well with those obtained by ELISA. We conclude that the SPR biosensor offers outstanding advantages for the MCs detection and may be further developed as a field-portable sensor for real-time monitoring of MCs on site in the near future.

‘Decoy peptide’ region (RIFLKRMPSI) of prorenin prosegment plays a crucial role in prorenin binding to the (pro)renin receptor

This study investigated a role of decoy peptide region (R10PIFLKRMPSI19P) in prorenin prosegment for prorenin binding to the (pro)renin receptor using the surface plasmon resonance technique. Three kinds of anti-receptor antibodies labeled as anti-107/121, anti-221/235 and anti-His tag antibody were prepared. The respective antigens D107SVANSIHSLFSEET121 (close to the N-terminal side of receptor), E221IGKRYGEDSEQFRD235 (N-terminal side of the transmembrane part of receptor) and 10xHis sequence (C-terminus) were designed based on the sequence of the receptor. These antibodies were immobilized on the CM5 sensor chip by amine coupling and allowed to bind to the receptor. Human prorenin, renin and the decoy bound to the receptor associated with antibodies. Their association (ka) and dissociation (kd) rate constants were measured and the dissociation constants (KD) were determined using Langmuir 1:1 kinetic binding model. The KD for interaction of prorenin and receptor associated to anti-107/121, anti-221/235 and anti-His tag antibodies were 2.9, 1.2 and 7.8 nM, respectively and for renin they were 9.3, 4.4 and 7.1 nM. The decoy bound to the respective immobilized receptor-antibody complexes at KD's of 6.2, 3.5 and 15.2 nM. Prorenin, renin and decoy had lower KD at the nanomolar ranges compared to those of L1PPTD4P in the prorenin prosegment and A248KKRLFDYVV257 in the C-domain of mature renin. The decoy reduced the binding of not only prorenin but also renin to (P)RR. These data are direct evidence that prorenin, renin and the peptides bind to (P)RR and the decoy reduces prorenin binding, supporting our hypothesis that decoy peptide region has a crucial role in prorenin binding.

Defining the Structural Basis of Human Plasminogen Binding by Streptococcal Surface Enolase

The flesh-eating bacterium group A Streptococcus (GAS) binds and activates human plasminogen, promoting invasive disease. Streptococcal surface enolase (SEN), a glycolytic pathway enzyme, is an identified plasminogen receptor of GAS. Here we used mass spectrometry (MS) to confirm that GAS SEN is octameric, thereby validating in silico modeling based on the crystal structure of Streptococcus pneumoniae alpha-enolase. Site-directed mutagenesis of surface-located lysine residues (SEN(K252 + 255A), SEN(K304A), SEN(K334A), SEN(K344E), SEN(K435L), and SEN(Delta434-435)) was used to examine their roles in maintaining structural integrity, enzymatic function, and plasminogen binding. Structural integrity of the GAS SEN octamer was retained for all mutants except SEN(K344E), as determined by circular dichroism spectroscopy and MS. However, ion mobility MS revealed distinct differences in the stability of several mutant octamers in comparison with wild type. Enzymatic analysis indicated that SEN(K344E) had lost alpha-enolase activity, which was also reduced in SEN(K334A) and SEN(Delta434-435). Surface plasmon resonance demonstrated that the capacity to bind human plasminogen was abolished in SEN(K252 + 255A), SEN(K435L), and SEN(Delta434-435). The lysine residues at positions 252, 255, 434, and 435 therefore play a concerted role in plasminogen acquisition. This study demonstrates the ability of combining in silico structural modeling with ion mobility-MS validation for undertaking functional studies on complex protein structures.

Polymeric Osteopontin Employs Integrin α9β1 as a Receptor and Attracts Neutrophils by Presenting a de Novo Binding Site

Osteopontin (OPN) is a cytokine and ligand for multiple members of the integrin family. OPN undergoes the in vivo polymerization catalyzed by cross-linking enzyme transglutaminase 2, which consequently increases the bioactivity through enhanced interaction with integrins. The integrin alpha9beta1, highly expressed on neutrophils, binds to the sequence SVVYGLR only after intact OPN is cleaved by thrombin. The SVVYGLR sequence appears to be cryptic in intact OPN because alpha9beta1 does not recognize intact OPN. Because transglutaminase 2-catalyzed polymers change their physical and chemical properties, we hypothesized that the SVVYGLR site might also be exposed on polymeric OPN. As expected, alpha9beta1 turned into a receptor for polymeric OPN, a result obtained by cell adhesion and migration assays with alpha9-transfected cells and by detection of direct binding of recombinant soluble alpha9beta1 with colorimetry and surface plasmon resonance analysis. Because the N-terminal fragment of thrombin-cleaved OPN, a ligand for alpha9beta1, has been reported to attract neutrophils, we next examined migration of neutrophils to polymeric OPN using time-lapse microscopy. Polymeric OPN showed potent neutrophil chemotactic activity, which was clearly inhibited by anti-alpha9beta1 antibody. Unexpectedly, mutagenesis studies showed that alpha9beta1 bound to polymeric OPN independently of the SVVYGLR sequence, and further, SVVYGLR sequence of polymeric OPN was cryptic because SVVYGLR-specific antibody did not recognize polymeric OPN. These results demonstrate that polymerization of OPN generates a novel alpha9beta1-binding site and that the interaction of this site with the alpha9beta1 integrin is critical to the neutrophil chemotaxis induced by polymeric OPN.

Mice Lacking the Extracellular Matrix Protein WARP Develop Normally but Have Compromised Peripheral Nerve Structure and Function

WARP is a recently identified extracellular matrix molecule with restricted expression in permanent cartilages and a distinct subset of basement membranes in peripheral nerves, muscle, and the central nervous system vasculature. WARP interacts with perlecan, and we also demonstrate here that WARP binds type VI collagen, suggesting a function in bridging connective tissue structures. To understand the in vivo function of WARP, we generated a WARP-deficient mouse strain. WARP-null mice were healthy, viable, and fertile with no overt abnormalities. Motor function and behavioral testing demonstrated that WARP-null mice exhibited a significantly delayed response to acute painful stimulus and impaired fine motor coordination, although general motor function was not affected, suggesting compromised peripheral nerve function. Immunostaining of WARP-interacting ligands demonstrated that the collagen VI microfibrillar matrix was severely reduced and mislocalized in peripheral nerves of WARP-null mice. Further ultrastructural analysis revealed reduced fibrillar collagen deposition within the peripheral nerve extracellular matrix and abnormal partial fusing of adjacent Schwann cell basement membranes, suggesting an important function for WARP in stabilizing the association of the collagenous interstitial matrix with the Schwann cell basement membrane. In contrast, other WARP-deficient tissues such as articular cartilage, intervertebral discs, and skeletal muscle showed no detectable abnormalities, and basement membranes formed normally. Our data demonstrate that although WARP is not essential for basement membrane formation or musculoskeletal development, it has critical roles in the structure and function of peripheral nerves.

Rapid Optimization of a Peptide Inhibitor of Malaria Parasite Invasion by Comprehensive N-Methyl Scanning

Apical membrane antigen 1 (AMA1) of the malaria parasite Plasmodium falciparum has been implicated in the invasion of host erythrocytes and is an important vaccine candidate. We have previously described a 20-residue peptide, R1, that binds to AMA1 and subsequently blocks parasite invasion. Because this peptide appears to target a site critical for AMA1 function, it represents an important lead compound for anti-malarial drug development. However, the effectiveness of this peptide inhibitor was limited to a subset of parasite isolates, indicating a requirement for broader strain specificity. Furthermore, a barrier to the utility of any peptide as a potential therapeutic is its susceptibility to rapid proteolytic degradation. In this study, we sought to improve the proteolytic stability and AMA1 binding properties of the R1 peptide by systematic methylation of backbone amides (N-methylation). The inclusion of a single N-methyl group in the R1 peptide backbone dramatically increased AMA1 affinity, bioactivity, and proteolytic stability without introducing global structural alterations. In addition, N-methylation of multiple R1 residues further improved these properties. Therefore, we have shown that modifications to a biologically active peptide can dramatically enhance activity. This approach could be applied to many lead peptides or peptide therapeutics to simultaneously optimize a number of parameters.

A radioisotope label-free α-bungarotoxin-binding assay using BIAcore sensor chip technology for real-time analysis

α-Bungarotoxin (α-bgtx)-binding proteins, including certain nicotinic acetylcholine receptors and acetylcholine-binding proteins (AChBPs), are frequently characterized with radioisotope-labeled α-bgtx-binding assays. Such assays, however, preclude investigations of binding interactions in real time and are hampered by the inconveniences associated with radioisotope-labeled reagents. We used surface plasmon resonance-based technology (BIAcore) to investigate the binding of recombinant AChBP to CM-5 sensor chip surfaces with directly immobilized α-bgtx. We validated our BIAcore results by comparing the same biological samples using the traditional 125I-labeled α-bgtx-binding assay. An α-bgtx sensor chip, as described here, enables detailed, real-time, radioisotope-free interaction studies that can greatly facilitate the characterization of novel α-bgtx-binding proteins and complexes.

Ribosomal Protein S19 Interacts with Macrophage Migration Inhibitory Factor and Attenuates Its Pro-inflammatory Function

Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine that has been implicated in the pathogenesis of inflammatory disorders such as infection, sepsis, and autoimmune disease. MIF exists preformed in cytoplasmic pools and exhibits an intrinsic tautomerase and oxidoreductase activity. MIF levels are elevated in the serum of animals and patients with infection or different inflammatory disorders. To elucidate how MIF actions are controlled, we searched for endogenous MIF-interacting proteins with the potential to interfere with key MIF functions. Using in vivo biotin-tagging and endogenous co-immunoprecipitation, the ribosomal protein S19 (RPS19) was identified as a novel MIF binding partner. Surface plasmon resonance and pulldown experiments with wild type and mutant MIF revealed a direct physical interaction of the two proteins (K(D) = 1.3 x 10(-6) m). As RPS19 is released in inflammatory lesions by apoptotic cells, we explored whether it affects MIF function and inhibits its binding to receptors CD74 and CXCR2. Low doses of RPS19 were found to strongly inhibit MIF-CD74 interaction. Furthermore, RPS19 significantly compromised CXCR2-dependent MIF-triggered adhesion of monocytes to endothelial cells under flow conditions. We, therefore, propose that RPS19 acts as an extracellular negative regulator of MIF.

Purification of Anti-HPA-1a Directly from Plasma Using Immobilised Recombinant HPA-1a Enables Determination of Antibody Affinity by Surface Plasmon Resonance Technology in Neonatal Alloimmune Thrombocytopenia.

Background: Most severe cases of neonatal alloimmune thrombocytopenia (NAIT) in the Caucasian population are due to anti-HPA-1a. The precise influences of antibody amount or affinity on severity of NAIT remain to be elucidated. In an earlier study, we assessed the interaction between anti-HPA-1a and HPA-1a antigen by surface plasmon resonance technology (SPRT) using IgG fractions recovered from antibody (ab) positive HPA-1b maternal sera using protein-A chromatography. However, high background in some of the IgG fractions prohibited the determination of antibody affinity (Bessos et al, Trans Apher Sci, In Press). The aim of this study was to investigate the affinity of anti-HPA-1a purified directly from plasma using immobilised HPA-1a antigen.Methods: Native glycoprotein (GP) IIb/IIIa was extracted and purified from HPA-1a1a platelet donors, while recombinant PSI domain of HPA-1a GPIIIa (rec-HPA-1a) was obtained by conventional cloning techniques. CNBr activated Sepharose 4B was coupled either with native GPIIb/IIIa or with rec-HPA-1a and used for the immunopurification of anti-HPA-1a directly from 4 female plasma samples positive for anti-HPA-1a ab. The plasma samples were pre-adsorbed with non-coupled Sepharose 4B prior to mixing with immobilised HPA-1a antigen. The acid eluted abs were dialysed, concentrated and assessed by ELISA (using HPA-1a GPIIb/IIIa coated plates), silver staining (using reduced gels) and SPRT-Biacore X, using CM5 sensor chips bound with HPA-1a1a or HPA-1b1b antigen at 600–800 response units (RU). GPIIIa AP3 monoclonal ab (Mab) & CamTran 007 recombinant anti-HPA-1a (r-anti-1a) were used as controls in SPRT. Affinity and dissociation constants (Ka and Kd respectively) of abs tested in serial doubling dilutions were determined using the computer software BIAevaluation 3.2 RC1 (Biacore) - Langmuir 1:1 mathematical model.Results: Control AP3 Mab bound to both HPA-1a & -1b chips in SPRT yielding respective Ka values of 2x105 & 1.7x104, and respective Kd values of 2.6x10−3 & 6.7x10−5; while control r-anti-1a bound specifically to HPA-1a chips yielding Ka and Kd of 2.9x105 & 8.3x10−4. Antibodies purified from plasma using immobilised rec-HPA-1a demonstrated higher binding in the ELISA and purer samples by silver staining (IgG heavy and light chains) compared to abs purified using immobilised native GP. This was reflected in SPRT where anti-HPA-1a purified using immobilised native GP exhibited high background that prohibited Ka and Kd determinations, whereas abs purified using immobilised rec-HPA- 1a bound specifically to HPA-1a chips, enabling Ka and Kd determinations which ranged from 6.9x103 to 7.9x104 for Ka, and from 1.3x10−4 to 3.4x10−4 for Kd. Anti-HPA-1a purified by immobilised rec-HPA-1a also interacted specifically with CM 5 sensor chips bound with rec-HPA-1a but not rec-HPA-1b, although with lower affinity constants compared to chips bound with native HPA-1a GP, yielding Ka of 4.2x102 to 9.1x103, & Kd of 3.4x10−3 to 8.6x10−5.Conclusion: This is the first report of the direct purification of anti-HPA-1a from plasma by immobilised HPA-1a antigen. Our study shows that immunopurification of plasma using immobilised rec-HPA-1a yields pure anti-HPA-1a antibodies that bind specifically in SPRT to chips coupled with both native or recombinant HPA-1a, allowing determination of antibody affinity and dissociation constants. This novel development would enable much needed analysis of anti-HPA-1a binding mechanisms in NAIT involving patients with different disease outcomes.

Dissociation of Activated Protein C Functions by Elimination of Protein S Cofactor Enhancement

Activated protein C (APC) plays a critical anticoagulant role in vivo by inactivating procoagulant factor Va and factor VIIIa and thus down-regulating thrombin generation. In addition, APC bound to the endothelial cell protein C receptor can initiate protease-activated receptor-1 (PAR-1)-mediated cytoprotective signaling. Protein S constitutes a critical cofactor for the anticoagulant function of APC but is not known to be involved in regulating APC-mediated protective PAR-1 signaling. In this study we utilized a site-directed mutagenesis strategy to characterize a putative protein S binding region within the APC Gla domain. Three single amino acid substitutions within the APC Gla domain (D35T, D36A, and A39V) were found to mildly impair protein S-dependent anticoagulant activity (<2-fold) but retained entirely normal cytoprotective activity. However, a single amino acid substitution (L38D) ablated the ability of protein S to function as a cofactor for this APC variant. Consequently, in assays of protein S-dependent factor Va proteolysis using purified proteins or in the plasma milieu, APC-L38D variant exhibited minimal residual anticoagulant activity compared with wild type APC. Despite the location of Leu-38 in the Gla domain, APC-L38D interacted normally with endothelial cell protein C receptor and retained its ability to trigger PAR-1 mediated cytoprotective signaling in a manner indistinguishable from that of wild type APC. Consequently, elimination of protein S cofactor enhancement of APC anticoagulant function represents a novel and effective strategy by which to separate the anticoagulant and cytoprotective functions of APC for potential therapeutic gain.

Dimer of 2,7-diamino-1,8-naphthyridine for the detection of mismatches formed by pyrimidine nucleotide bases

Discrimination of base mismatches from normal Watson–Crick base pairs in duplex DNA constitutes a key approach to the detection of single nucleotide polymorphisms (SNPs). We have developed a sensor for a surface plasmon resonance (SPR) assay system to detect G–G, A–A, and C–C mismatch duplexes by employing a surface upon which mismatch-binding ligands (MBLs) are immobilized. We synthesized a new MBL consisting of 2,7-diamino-1,8-naphthyridine (damND) and immobilized it onto a CM5 sensor chip to carry out the SPR assay of DNA duplexes containing a single-base mismatch. The SPR sensor with damND revealed strong responses to all C–C mismatches, and sequence-dependent C–T and T–T mismatches. Compared to ND- and naphthyridine-azaquinolone hybrid (NA)-immobilized sensor surfaces, with affinity to mismatches composed of purine nucleotide bases, the damND-immobilized surface was useful for the detection of the mismatches composed of pyrimidine nucleotide bases.

Heparan Sulfate Regulates Fibrillin-1 N- and C-terminal Interactions

Fibrillin-1 N- and C-terminal heparin binding sites have been characterized. An unprocessed monomeric N-terminal fragment (PF1) induced a very high heparin binding response, indicating heparin-mediated multimerization. Using PF1 deletion and short fragments, a heparin binding site was localized within the domain encoded by exon 7 after the first hybrid domain. Rodent embryonic fibroblasts adhered to PF1 and deletion fragments, and, when cells were plated on fibrillin-1 or fibronectin Arg-Gly-Asp cell-binding fragments, cells showed heparin-dependent spreading and focal contact formation in response to soluble PF1. Within domains encoded by exons 59-62 near the fibrillin-1 C terminus are novel conformation-dependent high affinity heparin and tropoelastin binding sites. Heparin disrupted tropoelastin binding but did not disrupt N- and C-terminal fibrillin-1 interactions. Thus, fibrillin-1 N-terminal interactions with heparin/heparan sulfate directly influence cell behavior, whereas C-terminal interactions with heparin/heparan sulfate regulate elastin deposition. These data highlight how heparin/heparan sulfate controls fibrillin-1 interactions.

Phosphorylation of Receptor-Mimic Tyrosine Peptide on Surface Plasmon Resonance Sensor Chip and Its Interaction with Downstream Proteins

Abstract Insulin-like growth factor type-I receptor (IGF-1R) signal pathway is critical in several physiological activities and some pathogenesis. IGF-1R derived nonphosphorylated peptide LYASVNPEY was immobilized on the surface of CM5 sensor chip specialized for surface plasmon resonance (SPR) biosensor. The peptide surface was treated with cell lysates containing or not containing IGF-1R kinase. The results show that using SPR biosensor PY20 can discriminate the different levels of peptide tyrosine phosphorylation (PTP) caused by different incubation times and different lysates. The effect of the PTP on peptide-protein interaction was further studied. The results demonstrated that only the phosphorylated peptide can interact with its downstream insulin receptor substrate-1 (IRS-1). The binding affinity (KA) and the association and dissociation kinetics (ka and kd) of the phosphorylated peptide with IRS-1 were measured by SPR biosensor, with the results of KA = (2.02 ± 0.08) × 108 M−1, ka = (2.30 ± 0.15) × 106 M−1 s−1 and kd = (1.14 ± 0.13) × 10−2 s−1, respectively. This new phosphorylation method of peptide that simulates cell receptor has the characteristics of real-time, speediness, label-free, and convenience for detection, which is instrumental for investigations on receptor phosphorylation signal pathways and drug screening against these signal pathways.

Physical and Functional Interaction between Human Oxidized Base-specific DNA Glycosylase NEIL1 and Flap Endonuclease 1

The S phase-specific activation of NEIL1 and not of the other DNA glycosylases responsible for repairing oxidatively damaged bases in mammalian genomes and the activation of NEIL1 by proliferating cell nuclear antigen (PCNA) suggested preferential action by NEIL1 in oxidized base repair during DNA replication. Here we show that NEIL1 interacts with flap endonuclease 1 (FEN-1), an essential component of the DNA replication. FEN-1 is present in the NEIL1 immunocomplex isolated from human cell extracts, and the two proteins colocalize in the nucleus. FEN-1 stimulates the activity of NEIL1 in vitro in excising 5-hydroxyuracil from duplex, bubble, forked, and single-stranded DNA substrates by up to 5-fold. The disordered region near the C terminus of NEIL1, which is dispensable for activity, is necessary and sufficient for high affinity binding to FEN-1 (K(D) approximately = 0.2 microm). The interacting interface of FEN-1 is localized in its disordered C-terminal region uniquely present in mammalian orthologs. Fine structure mapping identified several Lys and Arg residues in this region that form salt bridges with Asp and Glu residues in NEIL1. NEIL1 was previously shown to initiate single nucleotide excision repair, which does not require FEN-1 or PCNA. The present study shows that NEIL1 could also participate in strand displacement repair synthesis (long patch repair (LP-BER)) mediated by FEN-1 and stimulated by PCNA. Interaction between NEIL1 and FEN-1 is essential for efficient NEIL1-initiated LP-BER. These studies strongly implicate NEIL1 in a distinct subpathway of LP-BER in replicating genomes.